Abstract
In this chapter, we will analyze basic GWAS using gPLINK and HaploView, which are visual interfaces of the PLINK software. We will perform appropriate GWAS data set selection, obtain a summary of the statistics, and filter out data with a proper threshold. We will perform a GWAS and visualize the results with a Manhattan plot.
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- 1.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC(2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
Package: PLINK (including version number)
Author: Shaun Purcell
URL: ► http://pngu.mgh.harvard.edu/purcell/plink/
- 2.
Bibliography
Barrett JC et al (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265. Epub 2004 Aug 5
Purcell S et al (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3):559–575. Epub 2007 Jul 25
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Kim, J.H. (2019). GWAS Data Analysis. In: Genome Data Analysis. Learning Materials in Biosciences. Springer, Singapore. https://doi.org/10.1007/978-981-13-1942-6_16
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DOI: https://doi.org/10.1007/978-981-13-1942-6_16
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